Anwar al-Awlaki, a radical Muslim imam who ministered to at least three 9/11 hijackers, the Fort Hood shooter and the crotch-bomber, was taken into custody at JFK Airport on a felony arrest warrant in 2002.

Even though Awlaki had been on the FBI’s radar for years, he was let go, most likely because of intervention by Saudi Arabia, classified documents and interviews reveal. Now he continues to train new “martyrs” in Yemen.

“We were stunned” that he was let go, said Ray Fournier, a federal agent who has been tracking Awlaki as part of a joint terrorism task force. “He was a high-value target. Everybody was excited about the prospect of hooking this guy up under a [criminal] charge to motivate a conversation with him regarding his relationship with the [9/11] hijackers.”

Awlaki, 38, was born in New Mexico and raised as a teen in Yemen. Fournier, then a Diplomatic Security Service agent, discovered that he lied about his place of birth on an application for a US Agency for International Development grant, receiving $20,000 a year to attend engineering classes at Colorado State University in the early 1990s. Awlaki turned to radical Islam instead, preaching at mosques in Fort Collins, Colo., and San Diego.

He attracted the FBI’s attention in 1999, because of alleged contact with an al Qaeda agent who bought a satellite phone for Osama bin Laden. But the investigation was closed the next year because of lack of evidence.

While in San Diego, Fournier said, Awlaki met at his mosque with Nawaf al-Hazmi and Khalid al-Mihdhar, who would go on to hijack the plane that was crashed into the Pentagon on 9/11.

In early 2001, Awlaki took over the pulpit at the Saudi-funded Dar al-Hijrah Islamic Center, which is located in Virginia, not far from the Pentagon. Hazmi followed him there. He and another Saudi hijacker, Hani Hanjour, pilot of the plane that hit the Pentagon, got help from Awlaki’s mosque obtaining housing and identification.

In post-9/11 interviews with the FBI, Awlaki denied having contact with the hijackers in Virginia, and said that although he met with Hazmi several times in San Diego, he doesn’t remember any specifics of what they discussed. The FBI let Awlaki go, but he remained on a watch list.

Meanwhile, Fournier was working up a warrant on the passport violation related to Awlaki’s schooling. In 2002, Awlaki left the United States for England and later Saudi Arabia. On Oct. 10 of that year, he returned and was detained at JFK.

Fournier said that a passport-fraud conviction carries a maximum sentence of only six months, but it would have given investigators time to “play ball” with Awlaki — to see if they could tie him to other charges.

According to classified immigration records, however, agents at JFK were advised to “release” the detainee because the warrant had mysteriously “been pulled back” the day before. Awlaki was handed off to a “Saudi rep” to continue his journey to Washington, where he recruited other terrorists. Not long after, he fled to Yemen.

Why would Saudi Arabia get involved in Awlaki’s welfare? For one, he worked with the Saudi embassy as a tour guide for hajj pilgrimages, a position that requires connections in Riyadh. “You don’t just get permission to lead tours” on the Muslim holy pilgrimage, said Hale Smith, a reformed Muslim convert who traveled with Awlaki on hajj, and roomed with the “very hard-line Sunni” cleric in Mecca and Medina. “You have to be in with the Saudis.”

Justice Department officials maintain the fraud warrant was withdrawn simply because there wasn’t enough evidence to make the charges against Awlaki stick.

But letting Awlaki free, as authorities now know, only allowed him to spread the seeds of hate to other terrorists.

Awlaki also carried on e-mail conversations with Maj. Nidal Malik Hasan, who went on to kill 13 people at Fort Hood in November. And crotch bomber Umar Farouk Abdulmutallab met with Awlaki in Yemen last summer. During his trip to that country, he was fitted with the device for his terror attack.

US authorities now suspect Awlaki has moved from preaching terrorism to planning it.

He gets hundreds, if not thousands, of young Muslim men jacked up for jihad. Court records cite Awlaki and his Web site as the source of inspiration for much of the homegrown terror plaguing the country right now — including the Fort Dix Six, who plotted to kill US troops while posing as pizza delivery drivers.

How many other Abdulmutallabs and Hasans has he inspired? A Facebook page for Awlaki has 4,800 “fans.” And his videotaped sermons are sold as CD box sets at mosques and Islamic bookstores across America.

His capture and interrogation are wartime imperatives.

Paul Sperry is a Hoover Institution media fellow and author of “Infiltration.” His latest book is “Muslim Mafia.”

Free radical

American-born Anwar al-Awlaki has preached radical Islam to a who’s who of terrorists, including:

* FORT HOOD SHOOTER: Awlaki ministers to Maj. Nidal Malik Hasan (right), who also attends Dar al-Hijrah, in 2001. In 2008, Hasan contacts Awlaki by e-mail, asking him “about killing American soldiers and officers and whether that was legitimate or not.” It’s the first of some 20 e-mails between them. From Yemen, Awlaki praises him as a “hero” after Hasan kills 13 at Fort Hood.

* 9/11 HIJACKERS: Awlaki meets with Saudi hijackers Nawaf al-Hazmi and Khalid al-Mihdhar . who flew the hijacked plane into the Pentagon on 9/11 . at his Masjid al-Rabat mosque in San Diego in 2000. The next year, Awlaki takes over the pulpit at Saudi-funded Dar al-Hijrah Islamic Center in Virginia. Hazmi and another Saudi hijacker, Hani Hanjour, get help from Awlaki’s mosque obtaining housing and IDs.

* CROTCH BOMBER: Umar Farouk Abdulmutallab meets with Awlaki in Yemen last summer. NSA also picks up phone conversations between the two. Abdulmutallab tries to detonate a bomb hidden in his underwear while on a plane en route to Detroit on Christmas Day.